rs262929

Positions:

• chr6-37176628-A-G
• chr6-37176628-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.804 in 152,120 control chromosomes in the GnomAD database, including 49,293 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.80 (49293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122165 AN: 152002 Hom.: 49236 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.799

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.804 AC: 122282 AN: 152120 Hom.: 49293 Cov.: 32 AF XY: 0.805 AC XY: 59823 AN XY: 74358

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.798

Alfa AF: 0.796 Hom.: 49626

Bravo AF: 0.808

Asia WGS AF: 0.875 AC: 3043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs262929; hg19: chr6-37144404;